He really killed the real red john in 'strawberries and cream 2',  and has taken over the red john persona ever since.  So far the only ones he has killed is the serial killer Panzer and the murdering Todd Johnson, and I suspect he will use the red john moniker for a lot of mischief.  I think he is halucination some things like the 'tyger tyger' mumbled by Todd Johnson on his death bed, c'mon that guy wasn't saying anything...and possible he doesn't know himself that he is now the new red john.  The taped recording strapped to Wainright is the voice of Patrick Jane mimicing the voice of the real red john as he heard it in the 'tyger tyger burning bright' incident.